-package jalview.ws;
-
-import jalview.gui.AlignFrame;
-import jalview.gui.WebserviceInfo;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.Desktop;
-import javax.swing.JOptionPane;
-import jalview.bin.Cache;
-
-public abstract class WSThread extends Thread
-{
- /**
- * Generic properties for Web Service Client threads.
- */
- AlignFrame alignFrame;
- WebserviceInfo wsInfo = null;
- AlignmentView input;
- boolean jobComplete = false;
- abstract class WSJob {
- /**
- * Generic properties for an individual job within a Web Service Client thread
- */
- int jobnum = 0; // WebServiceInfo pane for this job
- String jobId; // ws job ticket
- boolean cancelled = false;
- int allowedServerExceptions = 3; // job dies if too many exceptions.
- boolean submitted = false;
- boolean subjobComplete = false;
- /**
- *
- * @return true if job has completed and valid results are available
- */
- abstract boolean hasResults();
- /**
- *
- * @return boolean true if job can be submitted.
- */
- abstract boolean hasValidInput();
- vamsas.objects.simple.Result result;
- }
- class JobStateSummary {
- int running = 0;
- int queuing = 0;
- int finished = 0;
- int error = 0;
- int serror = 0;
- int cancelled = 0;
- int results = 0;
- void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
- WSJob j)
- {
- if (j.result != null)
- {
- String progheader = "";
- // Parse state of job[j]
- if (j.result.isRunning())
- {
- running++;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
- }
- else if (j.result.isQueued())
- {
- queuing++;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
- }
- else if (j.result.isFinished())
- {
- finished++;
- j.subjobComplete = true;
- if (j.hasResults())
- results++;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
- }
- else if (j.result.isFailed())
- {
- progheader += "Job failed.\n";
- j.subjobComplete = true;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
- error++;
- }
- else if (j.result.isServerError())
- {
- serror++;
- j.subjobComplete = true;
- wsInfo.setStatus(j.jobnum,
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- else if (j.result.isBroken() || j.result.isFailed())
- {
- error++;
- j.subjobComplete = true;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
- }
- // and pass on any sub-job messages to the user
- wsInfo.setProgressText(j.jobnum, OutputHeader);
- wsInfo.appendProgressText(j.jobnum, progheader);
- if (j.result.getStatus() != null)
- {
- wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
- }
- }
- else
- {
- if (j.submitted && j.subjobComplete)
- {
- if (j.allowedServerExceptions == 0)
- {
- serror++;
- }
- else if (j.result == null)
- {
- error++;
- }
- }
- }
- }
- }
-
- WSJob jobs[] = null;
- String WebServiceName = null;
- String OutputHeader;
- String WsUrl = null;
- abstract void pollJob(WSJob job) throws Exception;
- public void run()
- {
- JobStateSummary jstate=null;
- if (jobs==null)
- jobComplete=true;
- while (!jobComplete)
- {
- jstate = new JobStateSummary();
- for (int j = 0; j < jobs.length; j++)
- {
-
- if (!jobs[j].submitted && jobs[j].hasValidInput())
- {
- StartJob(jobs[j]);
- }
-
- if (jobs[j].submitted && !jobs[j].subjobComplete)
- {
- try
- {
- pollJob(jobs[j]);
- if (jobs[j].result == null)
- {
- throw (new Exception(
- "Timed out when communicating with server\nTry again later.\n"));
- }
- jalview.bin.Cache.log.debug("Job " + j + " Result state " +
- jobs[j].result.getState()
- + "(ServerError=" +
- jobs[j].result.isServerError() + ")");
- }
- catch (Exception ex)
- {
- // Deal with Transaction exceptions
- wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
- + " Server exception!\n" + ex.getMessage());
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
- + ") Server exception: " + ex.getMessage());
-
- if (jobs[j].allowedServerExceptions > 0)
- {
- jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
- try
- {
- Thread.sleep(5000);
- }
- catch (InterruptedException ex1)
- {
- }
- }
- else
- {
- Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
- jobs[j].subjobComplete = true;
- wsInfo.setStatus(jobs[j].jobnum,
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
- catch (OutOfMemoryError er)
- {
- jobComplete = true;
- jobs[j].subjobComplete = true;
- jobs[j].result = null; // may contain out of date result object
- wsInfo.setStatus(jobs[j].jobnum,
- WebserviceInfo.STATE_STOPPED_ERROR);
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Out of memory handling result for job !!"
- +
- "\nSee help files for increasing Java Virtual Machine memory.",
- "Out of memory", JOptionPane.WARNING_MESSAGE);
- Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
- WsUrl + "/" + jobs[j].jobId, er);
- System.gc();
- }
- }
- jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
- }
- // Decide on overall state based on collected jobs[] states
- if (jstate.running > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- }
- else if (jstate.queuing > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
- }
- else
- {
- jobComplete = true;
- if (jstate.finished > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- }
- else if (jstate.error > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- }
- else if (jstate.serror > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
- if (!jobComplete)
- {
- try
- {
- Thread.sleep(5000);
- }
- catch (InterruptedException e)
- {
- Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
- }
- // System.out.println("I'm alive "+alTitle);
- }
- }
- if (jobComplete)
- {
- parseResult(); // tidy up and make results available to user
- }
-}
-abstract void StartJob(WSJob job);
-abstract void parseResult();
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.ws;\r
+\r
+import javax.swing.*;\r
+\r
+import jalview.bin.*;\r
+import jalview.datamodel.*;\r
+import jalview.gui.*;\r
+import jalview.gui.FeatureRenderer.FeatureRendererSettings;\r
+\r
+public abstract class WSThread extends Thread\r
+{\r
+ /**\r
+ * Generic properties for Web Service Client threads.\r
+ */\r
+ /**\r
+ * view that this job was associated with\r
+ */\r
+ AlignmentI currentView = null;\r
+\r
+ /**\r
+ * feature settings from view that job was associated with\r
+ */\r
+ FeatureRendererSettings featureSettings = null;\r
+\r
+ /**\r
+ * metadata about this web service\r
+ */\r
+ WebserviceInfo wsInfo = null;\r
+\r
+ /**\r
+ * original input data for this job\r
+ */\r
+ AlignmentView input = null;\r
+\r
+ /**\r
+ * dataset sequence relationships to be propagated onto new results\r
+ */\r
+ AlignedCodonFrame[] codonframe = null;\r
+\r
+ /**\r
+ * are there jobs still running in this thread.\r
+ */\r
+ boolean jobComplete = false;\r
+\r
+ abstract class WSJob\r
+ {\r
+ /**\r
+ * Generic properties for an individual job within a Web Service Client\r
+ * thread\r
+ */\r
+ int jobnum = 0; // WebServiceInfo pane for this job\r
+\r
+ String jobId; // ws job ticket\r
+\r
+ /**\r
+ * has job been cancelled\r
+ */\r
+ boolean cancelled = false;\r
+\r
+ /**\r
+ * number of exceptions left before job dies\r
+ */\r
+ int allowedServerExceptions = 3;\r
+\r
+ /**\r
+ * has job been submitted\r
+ */\r
+ boolean submitted = false;\r
+\r
+ /**\r
+ * are all sub-jobs complete\r
+ */\r
+ boolean subjobComplete = false;\r
+\r
+ /**\r
+ * \r
+ * @return true if job has completed and valid results are available\r
+ */\r
+ abstract boolean hasResults();\r
+\r
+ /**\r
+ * \r
+ * @return boolean true if job can be submitted.\r
+ */\r
+ abstract boolean hasValidInput();\r
+\r
+ /**\r
+ * The last result object returned by the service.\r
+ */\r
+ vamsas.objects.simple.Result result;\r
+ }\r
+\r
+ class JobStateSummary\r
+ {\r
+ /**\r
+ * number of jobs running\r
+ */\r
+ int running = 0;\r
+\r
+ /**\r
+ * number of jobs queued\r
+ */\r
+ int queuing = 0;\r
+\r
+ /**\r
+ * number of jobs finished\r
+ */\r
+ int finished = 0;\r
+\r
+ /**\r
+ * number of jobs failed\r
+ */\r
+ int error = 0;\r
+\r
+ /**\r
+ * number of jobs stopped due to server error\r
+ */\r
+ int serror = 0;\r
+\r
+ /**\r
+ * number of jobs cancelled\r
+ */\r
+ int cancelled = 0;\r
+\r
+ /**\r
+ * number of jobs finished with results\r
+ */\r
+ int results = 0;\r
+\r
+ /**\r
+ * processes WSJob and updates job status counters and WebService status\r
+ * displays\r
+ * \r
+ * @param wsInfo\r
+ * @param OutputHeader\r
+ * @param j\r
+ */\r
+ void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,\r
+ WSJob j)\r
+ {\r
+ if (j.result != null)\r
+ {\r
+ String progheader = "";\r
+ // Parse state of job[j]\r
+ if (j.result.isRunning())\r
+ {\r
+ running++;\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);\r
+ }\r
+ else if (j.result.isQueued())\r
+ {\r
+ queuing++;\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);\r
+ }\r
+ else if (j.result.isFinished())\r
+ {\r
+ finished++;\r
+ j.subjobComplete = true;\r
+ if (j.hasResults())\r
+ {\r
+ results++;\r
+ }\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);\r
+ }\r
+ else if (j.result.isFailed())\r
+ {\r
+ progheader += "Job failed.\n";\r
+ j.subjobComplete = true;\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
+ error++;\r
+ }\r
+ else if (j.result.isServerError())\r
+ {\r
+ serror++;\r
+ j.subjobComplete = true;\r
+ wsInfo.setStatus(j.jobnum,\r
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ }\r
+ else if (j.result.isBroken() || j.result.isFailed())\r
+ {\r
+ error++;\r
+ j.subjobComplete = true;\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
+ // and pass on any sub-job messages to the user\r
+ wsInfo.setProgressText(j.jobnum, OutputHeader);\r
+ wsInfo.appendProgressText(j.jobnum, progheader);\r
+ if (j.result.getStatus() != null)\r
+ {\r
+ wsInfo.appendProgressText(j.jobnum, j.result.getStatus());\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (j.submitted && j.subjobComplete)\r
+ {\r
+ if (j.allowedServerExceptions == 0)\r
+ {\r
+ serror++;\r
+ }\r
+ else if (j.result == null)\r
+ {\r
+ error++;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * one or more jobs being managed by this thread.\r
+ */\r
+ WSJob jobs[] = null;\r
+\r
+ /**\r
+ * full name of service\r
+ */\r
+ String WebServiceName = null;\r
+\r
+ String OutputHeader;\r
+\r
+ String WsUrl = null;\r
+\r
+ /**\r
+ * query web service for status of job. on return, job.result must not be null\r
+ * - if it is then it will be assumed that the job status query timed out and\r
+ * a server exception will be logged.\r
+ * \r
+ * @param job\r
+ * @throws Exception\r
+ * will be logged as a server exception for this job\r
+ */\r
+ abstract void pollJob(WSJob job) throws Exception;\r
+\r
+ public void run()\r
+ {\r
+ JobStateSummary jstate = null;\r
+ if (jobs == null)\r
+ {\r
+ jobComplete = true;\r
+ }\r
+ while (!jobComplete)\r
+ {\r
+ jstate = new JobStateSummary();\r
+ for (int j = 0; j < jobs.length; j++)\r
+ {\r
+\r
+ if (!jobs[j].submitted && jobs[j].hasValidInput())\r
+ {\r
+ StartJob(jobs[j]);\r
+ }\r
+\r
+ if (jobs[j].submitted && !jobs[j].subjobComplete)\r
+ {\r
+ try\r
+ {\r
+ pollJob(jobs[j]);\r
+ if (jobs[j].result == null)\r
+ {\r
+ throw (new Exception(\r
+ "Timed out when communicating with server\nTry again later.\n"));\r
+ }\r
+ jalview.bin.Cache.log.debug("Job " + j + " Result state "\r
+ + jobs[j].result.getState() + "(ServerError="\r
+ + jobs[j].result.isServerError() + ")");\r
+ } catch (Exception ex)\r
+ {\r
+ // Deal with Transaction exceptions\r
+ wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName\r
+ + " Server exception!\n" + ex.getMessage());\r
+ Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum\r
+ + ") Server exception: " + ex.getMessage());\r
+\r
+ if (jobs[j].allowedServerExceptions > 0)\r
+ {\r
+ jobs[j].allowedServerExceptions--;\r
+ Cache.log.debug("Sleeping after a server exception.");\r
+ try\r
+ {\r
+ Thread.sleep(5000);\r
+ } catch (InterruptedException ex1)\r
+ {\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);\r
+ jobs[j].subjobComplete = true;\r
+ wsInfo.setStatus(jobs[j].jobnum,\r
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ }\r
+ } catch (OutOfMemoryError er)\r
+ {\r
+ jobComplete = true;\r
+ jobs[j].subjobComplete = true;\r
+ jobs[j].result = null; // may contain out of date result object\r
+ wsInfo.setStatus(jobs[j].jobnum,\r
+ WebserviceInfo.STATE_STOPPED_ERROR);\r
+ Cache.log.error("Out of memory when retrieving Job " + j\r
+ + " id:" + WsUrl + "/" + jobs[j].jobId, er);\r
+ new jalview.gui.OOMWarning("retrieving result for "\r
+ + WebServiceName, er);\r
+ System.gc();\r
+ }\r
+ }\r
+ jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);\r
+ }\r
+ // Decide on overall state based on collected jobs[] states\r
+ if (jstate.running > 0)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+ }\r
+ else if (jstate.queuing > 0)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ }\r
+ else\r
+ {\r
+ jobComplete = true;\r
+ if (jstate.finished > 0)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ }\r
+ else if (jstate.error > 0)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
+ else if (jstate.serror > 0)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ }\r
+ }\r
+ if (!jobComplete)\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(5000);\r
+ } catch (InterruptedException e)\r
+ {\r
+ Cache.log\r
+ .debug("Interrupted sleep waiting for next job poll.", e);\r
+ }\r
+ // System.out.println("I'm alive "+alTitle);\r
+ }\r
+ }\r
+ if (jobComplete && jobs != null)\r
+ {\r
+ parseResult(); // tidy up and make results available to user\r
+ }\r
+ else\r
+ {\r
+ Cache.log\r
+ .debug("WebServiceJob poll loop finished with no jobs created.");\r
+ wsInfo.setFinishedNoResults();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * submit job to web service\r
+ * \r
+ * @param job\r
+ */\r
+ abstract void StartJob(WSJob job);\r
+\r
+ /**\r
+ * process the set of WSJob objects into a set of results, and tidy up.\r
+ */\r
+ abstract void parseResult();\r
+\r
+ /**\r
+ * helper function to conserve dataset references to sequence objects returned\r
+ * from web services 1. Propagates AlCodonFrame data from\r
+ * <code>codonframe</code> to <code>al</code>\r
+ * \r
+ * @param al\r
+ */\r
+ protected void propagateDatasetMappings(Alignment al)\r
+ {\r
+ if (codonframe != null)\r
+ {\r
+ SequenceI[] alignment = al.getSequencesArray();\r
+ for (int sq = 0; sq < alignment.length; sq++)\r
+ {\r
+ for (int i = 0; i < codonframe.length; i++)\r
+ {\r
+ if (codonframe[i] != null\r
+ && codonframe[i].involvesSequence(alignment[sq]))\r
+ {\r
+ al.addCodonFrame(codonframe[i]);\r
+ codonframe[i] = null;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param alignFrame\r
+ * reference for copying mappings across\r
+ * @param wsInfo\r
+ * gui attachment point\r
+ * @param input\r
+ * input data for the calculation\r
+ * @param webServiceName\r
+ * name of service\r
+ * @param wsUrl\r
+ * url of the service being invoked\r
+ */\r
+ public WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,\r
+ AlignmentView input, String webServiceName, String wsUrl)\r
+ {\r
+ this(alignFrame, wsinfo, input, wsUrl);\r
+ WebServiceName = webServiceName;\r
+ }\r
+\r
+ char defGapChar = '-';\r
+\r
+ /**\r
+ * \r
+ * @return gap character to use for any alignment generation\r
+ */\r
+ public char getGapChar()\r
+ {\r
+ return defGapChar;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param alframe\r
+ * - reference for copying mappings and display styles across\r
+ * @param wsinfo2\r
+ * - gui attachment point\r
+ * @param alview\r
+ * - input data for the calculation\r
+ * @param wsurl2\r
+ * - url of the service being invoked\r
+ */\r
+ public WSThread(AlignFrame alframe, WebserviceInfo wsinfo2,\r
+ AlignmentView alview, String wsurl2)\r
+ {\r
+ super();\r
+ // this.alignFrame = alframe;\r
+ currentView = alframe.getCurrentView().getAlignment();\r
+ featureSettings = alframe.getFeatureRenderer().getSettings();\r
+ defGapChar = alframe.getViewport().getGapCharacter();\r
+ this.wsInfo = wsinfo2;\r
+ this.input = alview;\r
+ WsUrl = wsurl2;\r
+ if (alframe != null)\r
+ {\r
+ AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()\r
+ .getCodonFrames();\r
+ if (cf != null)\r
+ {\r
+ codonframe = new AlignedCodonFrame[cf.length];\r
+ System.arraycopy(cf, 0, codonframe, 0, cf.length);\r
+ }\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff